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¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.

2D NMR: Overview of Homonuclear Correlation Techniques

2D NMR: Overview of Homonuclear Correlation Techniques

Homonuclear correlation spectroscopy (COSY) is a powerful technique used in Nuclear Magnetic Resonance (NMR) spectroscopy to study the correlations between nuclei of the same type within a molecule. It provides information about scalar couplings between adjacent nuclei, which helps determine connectivity and structural information. There are several COSY variants, each with its unique strengths and experimental parameters.
COSY90 is the standard two-dimensional (2D) COSY experiment that...

Two-Dimensional (2D) NMR: Overview

Two-Dimensional (2D) NMR: Overview

The 1D NMR spectrum of large and complex molecules like natural products has complicated splitting patterns and overlapping signals, which can be easily interpreted using 2-dimensional (2D) NMR. Unlike 1D NMR, 2D NMR has two frequency axes that provide the coupling information between the nucleus A and nucleus B in a molecule. The process from which 2D spectra are obtained has four steps.
The first step is the preparation period, during which nucleus A is excited with a radiofrequency pulse.

2D NMR: Overview of Heteronuclear Correlation Techniques

2D NMR: Overview of Heteronuclear Correlation Techniques

Heteronuclear correlation spectroscopy is an analytical technique that investigates the coupling between different types of nuclei, often a proton and an X-nucleus, such as carbon-13 or nitrogen-15. This method is commonly used in nuclear magnetic resonance (NMR) spectroscopy to gain insights into complex chemical compounds' structural and compositional aspects. A typical heteronuclear correlation spectrum displays X-nucleus chemical shifts on one axis and a proton spectrum on the other axis.

2D NMR: Homonuclear Correlation Spectroscopy (COSY)

2D NMR: Homonuclear Correlation Spectroscopy (COSY)

Homonuclear correlation spectroscopy, or COSY, is a 2-dimensional NMR technique that provides information about coupled protons. Typically, the geminal and vicinal coupling are observed. For example, consider the COSY spectrum of ethyl acetate, where its 1D proton NMR spectrum is plotted along the vertical and horizontal axes with their corresponding chemical shift scale. Three spots on the diagonal corresponding to the three peaks in the 1D proton spectrum are called diagonal peaks. The COSY...

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Updated: Jun 2, 2026

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Published on: September 17, 2017

Grid computing for improving conformational sampling in NMR structure calculation.

Fabien Mareuil¹, Christophe Blanchet, Thérèse E Malliavin

¹Unité de Bioinformatique Structurale, CNRS URA 2185, Institut Pasteur 25-28 rue du Dr Roux, F-75724 Paris Cedex 15, France.

Bioinformatics (Oxford, England)

|May 7, 2011

Summary

This summary is machine-generated.

This study adapted the Ambiguous Restraints for Iterative Assignment (ARIA) software for grid computing. This enables faster processing of complex nuclear magnetic resonance (NMR) data, improving protein structure determination.

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Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

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Structure and Coordination Determination of Peptide-metal Complexes Using 1D and 2D 1H NMR

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Published on: December 16, 2013

Area of Science:

Biophysics
Computational Biology
Structural Biology

Background:

Nuclear Magnetic Resonance (NMR) spectroscopy presents challenges in structure determination due to spectral ambiguities, particularly in solid-state NMR and for partially unfolded proteins.
Automatic structure determination methods often involve time-consuming calculations to resolve these ambiguities.
The Ambiguous Restraints for Iterative Assignment (ARIA) software was developed to aid in this process.

Purpose of the Study:

To enhance the computational power available for ARIA calculations.
To address the limitations of processing highly ambiguous NMR datasets.
To improve the efficiency and scope of protein structure determination using NMR.

Main Methods:

Adaptation of the ARIA software package for grid computing environments.
Utilization of middleware such as glite and Job Description Language (JDL) scripts for grid implementation.
Leveraging distributed computational power for conformational sampling.

Main Results:

The adapted ARIA software can be efficiently implemented on grid computing infrastructure.
Grid-enabled ARIA facilitates the analysis of highly ambiguous NMR datasets.
Increased computational power allows for significantly larger conformational sampling, leading to more robust structure determination.

Conclusions:

Grid computing provides a powerful platform for accelerating ARIA calculations.
This approach significantly enhances the ability to determine structures from challenging NMR data.
The enhanced ARIA version improves the efficiency and accuracy of protein structure determination.